Physical mapping of genomes, e.g., using restriction enzymes to develop restriction maps, can provide accurate information about the nucleic acids of various organisms. Restriction maps of, e.g., deoxyribonucleic acid (DNA), can be generated by optical mapping. Optical mapping can produce ordered restriction maps by using fluorescence microscopy to visualize restriction endonuclease cutting events on individual labeled DNA molecules. Generally, internal standards are used to size the nucleic acid molecules digested by restriction enzymes.